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Restoring missing apps after an incomplete iCloud restore

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Q: I recently bought a new iPhone 5 after my iPhone 4 was stolen and was attempting to restore my data using iCloud, following the steps in your Guide to Transferring your Content to a new iPhone, iPad or iPod touch. It seemed to go fine at first, but after my iPhone rebooted and the apps started loading, I got a “Restore Incomplete” message. Your article says that this is because some apps may not be available on the App Store, but at least one that didn’t reinstall still appears to be there, so I don’t know why it didn’t come down to my iPhone. My question, however, is if I reinstall these apps from the App Store or iTunes manually, will I lose the data in them? I haven’t backed up my iPhone to iTunes in months, and I don’t have the old iPhone anymore, so my iCloud backup is kind of all I’ve got. I still have all my apps on my computer, but I don’t normally sync that way, and don’t want to get all of the old data back with them. What should I do?

- Josh

A: The first phase of the iCloud restore, prior to your iPhone restarting, actually restores all of your application data from your iCloud backup. While this may seem backward, basically the data is loaded first, and then the apps follow.

This means that even though the apps in question haven’t been reinstalled, their data is still on your iPhone, waiting for the apps to arrive. If the exact same version of the app is actually still available on the App Store, you can certainly try reinstalling it this way, but keep in mind that some developers release updates as completely new apps, rather than updates to existing ones. This is why you may be able to find the app on the App Store, but the iCloud restore process cannot.

Ideally, restoring the app from iTunes is your best option since that’s much more likely to be the proper version. That said, if you don’t normally sync your iPhone to iTunes or update your apps there, it’s also possible that the one in iTunes may be older than what was on your iPhone. While you can check for updates in iTunes to try and download the latest versions, if an app isn’t available on the App Store any more, that won’t work any more than your iCloud restore did in terms of getting the app.

If you’ve synced your apps with your iTunes library in the past, getting them back onto your iPhone should simply be a matter of plugging it into iTunes and letting it sync; the missing apps will be transferred over as part of that process. If you don’t normally sync your apps with iTunes, however, you may will need to specifically select the ones you want added.

If you’re running a version of iTunes prior to iTunes 11, this can be somewhat tricky, as it requires enabling the “Sync” option on the Apps screen for your iPhone and then re-selecting ALL of the apps that should be on your device in order to avoid removing any. Fortunately, iTunes 11 made this process much simpler: iTunes will now detect what’s already on your iPhone and you’ll simply need to click the “Install” button beside those apps that you want to add.